Two Independent HIV Epidemics in Saint Petersburg, Russia Revealed by Molecular Epidemiology

Abstract

The HIV epidemic in Russia, one of the world's fastest growing, has been concentrated mostly among people who inject drugs (PWID). We sought to explore the epidemiology of the epidemic in St. Petersburg by sampling from the highest risk groups of PWID and men who have sex with men (MSM) and use viral sequencing data to better understand the nature of the city's epidemic. Serological testing confirmed an HIV prevalence among PWID in excess of 40%. All but 1 of 110 PWID whose blood samples were tested for genetic diversity were infected by subtype A virus, specifically by the AFSU strain. The remaining person was infected with a CRF-06cpx recombinant. Analysis of pairwise genetic distance among all PWID studied revealed an average of 3.1% sequence divergence, suggesting clonal introduction of the AFSU strain and/or constraints on sequence divergence. The HIV prevalence was less than 10% among MSM. All 17 sequences from HIV-infected MSM were found to be a clade B virus with a much higher average sequence diversity of 15.7%. These findings suggest two independent epidemics with little overlap between the two highest at-risk populations, which will require different HIV prevention approaches.

FIG. 1.

Phylogenetic analysis of the plasma-derived env fragments of HIV-1 subtype A. Closed triangles mark the sequences obtained from blood samples of people who inject drugs (PWID) who were HIV positive for less than 6 months (recent infection cases); closed circles show the sequences obtained from blood samples of PWID who were HIV positive for 12 month or more (chronic infection cases); open squares represent the strains obtained from PWID with an unknown duration of infection. For convenience, all titles of SATH-CAP sequences start with the two digits of the sampling year (2006, 07, or 08); titles of recent and chronic infection cases end with r or c, respectively. Unlabeled branches show the subtype A reference strains.

FIG. 2.

Nucleotide and amino acid diversity of HIV-1 subtype A and B env fragments. (A) Genetic diversity of recently transmitted subtype A strains is lower than that of persistent subtype A and B strains. Patterned bars represent the p-distance values obtained for the nucleotide sequences derived from two subgroups of subtype A: infected PWID and recent and chronic infection cases; open bar represents the values obtained for the nucleotide sequences of subtype B-infected men who have sex with men (MSM). (B) Amino acid diversity of recently transmitted subtype A strains is lower than that of persistent subtype A and B strains. Patterned bars represent the p-distance values obtained for the amino acid sequences derived from two subgroups of subtype A-infected PWID (recent and chronic infection cases); open bar represents the values obtained for the nucleotide sequences of subtype B-infected MSM.

FIG. 3.

Phylogenetic analysis of the plasma-derived env fragments of HIV-1 subtype B. Closed triangles indicate the sequences obtained from the blood samples of MSM within our study; other branches represent the subtype B reference strains and subtype A outgroup. For convenience, all titles of SATH-CAP sequences start with the two digits of the sampling year (2006, 07, or 08).